Adds a test for RaSP (which will get skipped in the action, unfortuna…

…tely)

examples/saturation_mutagenesis_for_two_proteins_using_rasp/saturation_mutagenesis_at_first_position.py

@@ -39,7 +39,10 @@ def saturation_mutagenesis_for_protein_at_position(
 
 
 if __name__ == "__main__":
-    wildtype_pdb_paths_for_rasp = list((THIS_DIR / "two_proteins").glob("*.pdb"))
+    wildtype_pdb_paths_for_rasp = [
+        THIS_DIR / "two_proteins" / "3ned.pdb",
+        THIS_DIR / "two_proteins" / "2vae.pdb",
+    ]
 
     _, f_rasp, x0, y0, _ = objective_factory.create(
         name="rasp",
@@ -74,4 +77,5 @@ def saturation_mutagenesis_for_protein_at_position(
         ]
     )
 
-    print(df.head())
+    print(df.head(20))
+    print(df.values[:20, 1])

src/poli/core/util/proteins/rasp/inner_rasp/LICENSE.txt

@@ -0,0 +1,13 @@
+Copyright 2022 - University of Copenhagen
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

src/poli/core/util/proteins/rasp/rasp_interface.py

@@ -20,6 +20,11 @@
 so you will only need internet access once.
 
 [1] TODO: add.
+[2] TODO: add.
+
+RaSP's source code was provided with an Apache 2.0 license. Modifications
+from the source have been duly noted. Most of the source code can be found
+at ./inner_rasp.
 """
 
 from typing import List
@@ -60,8 +65,15 @@
 
 
 class RaspInterface:
-    def __init__(self, working_dir: Path, verbose: bool = False) -> None:
+    def __init__(
+        self,
+        working_dir: Path,
+        verbose: bool = False,
+        verify_integrity_of_download: bool = True,
+    ) -> None:
         self.working_dir = working_dir
+        self.verbose = verbose
+        self.verify_integrity_of_download = verify_integrity_of_download
 
         # Making the appropriate folders:
         (self.working_dir / "raw").mkdir(parents=True, exist_ok=True)
@@ -81,7 +93,9 @@ def __init__(self, working_dir: Path, verbose: bool = False) -> None:
         # Downloading the cavity and downstream models.
         # TODO: should we be doing this eagerly? Or should
         # we wait to download and install it until we need it?
-        self.download_cavity_and_downstream_models(verbose=verbose)
+        self.download_cavity_and_downstream_models(
+            verbose=verbose, verify_integrity_of_download=verify_integrity_of_download
+        )
 
     def get_and_compile_reduce(self):
         """
@@ -190,7 +204,7 @@ def predict(
         return df_total
 
     def download_cavity_and_downstream_models(
-        self, verbose: bool = False, strict: bool = True
+        self, verbose: bool = False, verify_integrity_of_download: bool = True
     ):
         """
         This function downloads the cavity and downstream models
@@ -250,7 +264,7 @@ def download_cavity_and_downstream_models(
                 downloaded_md5_checksum
                 != precomputed_model_md5_checksums[cavity_model_path]
             ):
-                if strict:
+                if verify_integrity_of_download:
                     raise RuntimeError(
                         "The downloaded cavity model does not match the expected md5 checksum. "
                         "This could be due to a corrupted download, or a malicious attack. "
@@ -285,7 +299,7 @@ def download_cavity_and_downstream_models(
                     downloaded_md5_checksum
                     != precomputed_model_md5_checksums[path_.parent.name]
                 ):
-                    if strict:
+                    if verify_integrity_of_download:
                         raise RuntimeError(
                             f"The downloaded downstream model {path_.parent.name} does not match the expected md5 checksum. "
                             "This could be due to a corrupted download, or a malicious attack. "